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Chheda J, Fang Y, Deriu C, Ezzat AA, Fabris L. Discrimination of Genetic Biomarkers of Disease through Machine-Learning-Based Hypothesis Testing of Direct SERS Spectra of DNA and RNA. ACS Sens 2024; 9:2488-2498. [PMID: 38684231 DOI: 10.1021/acssensors.4c00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Cancer is globally a leading cause of death that would benefit from diagnostic approaches detecting it in its early stages. However, despite much research and investment, cancer early diagnosis is still underdeveloped. Owing to its high sensitivity, surface-enhanced Raman spectroscopy (SERS)-based detection of biomarkers has attracted growing interest in this area. Oligonucleotides are an important type of genetic biomarkers as their alterations can be linked to the disease prior to symptom onset. We propose a machine-learning (ML)-enabled framework to analyze complex direct SERS spectra of short, single-stranded DNA and RNA targets to identify relevant mutations occurring in genetic biomarkers, which are key disease indicators. First, by employing ad hoc-synthesized colloidal silver nanoparticles as SERS substrates, we analyze single-base mutations in ssDNA and RNA sequences using a direct SERS-sensing approach. Then, an ML-based hypothesis test is proposed to identify these changes and differentiate the mutated sequences from the corresponding native ones. Rooted in "functional data analysis," this ML approach fully leverages the rich information and dependencies within SERS spectral data for improved modeling and detection capability. Tested on a large set of DNA and RNA SERS data, including from miR-21 (a known cancer miRNA biomarker), our approach is shown to accurately differentiate SERS spectra obtained from different oligonucleotides, outperforming various data-driven methods across several performance metrics, including accuracy, sensitivity, specificity, and F1-scores. Hence, this work represents a step forward in the development of the combined use of SERS and ML as effective methods for disease diagnosis with real applicability in the clinic.
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Affiliation(s)
- Jinisha Chheda
- Department of Materials Science and Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Yating Fang
- Department of Industrial and Systems Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Chiara Deriu
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Ahmed Aziz Ezzat
- Department of Industrial and Systems Engineering, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Laura Fabris
- Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
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Geng X, Zhou ZA, Mi Y, Wang C, Wang M, Guo C, Qu C, Feng S, Kim I, Yu M, Ji H, Ren X. Glioma Single-Cell Biomechanical Analysis by Cyclic Conical Constricted Microfluidics. Anal Chem 2023; 95:15585-15594. [PMID: 37843131 DOI: 10.1021/acs.analchem.3c02434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2023]
Abstract
Determining the grade of glioma is a critical step in choosing patients' treatment plans in clinical practices. The pathological diagnosis of patient's glioma samples requires extensive staining and imaging procedures, which are expensive and time-consuming. Current advanced uniform-width-constriction-channel-based microfluidics have proven to be effective in distinguishing cancer cells from normal tissues, such as breast cancer, ovarian cancer, prostate cancer, etc. However, the uniform-width-constriction channels can result in low yields on glioma cells with irregular morphologies and high heterogeneity. In this research, we presented an innovative cyclic conical constricted (CCC) microfluidic device to better differentiate glioma cells from normal glial cells. Compared with the widely used uniform-width-constriction microchannels, the new CCC configuration forces single cells to deform gradually and obtains the biophysical attributes from each deformation. The human-derived glioma cell lines U-87 and U-251, as well as the human-derived normal glial astrocyte cell line HA-1800 were selected as the proof of concept. The results showed that CCC channels can effectively obtain the biomechanical characteristics of different 12-25 μm glial cell lines. The patient glioma samples with WHO grades II, III, and IV were tested by CCC channels and compared between Elastic Net (ENet) and Lasso analysis. The results demonstrated that CCC channels and the ENet can successfully select critical biomechanical parameters to differentiate the grades of single-glioma cells. This CCC device can be potentially further applied to the extensive family of brain tumors at the single-cell level.
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Affiliation(s)
- Xin Geng
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Zi-Ang Zhou
- Department of Microelectronics, Tianjin University, Tianjin 300072, China
| | - Yang Mi
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chunhong Wang
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Meng Wang
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chenjia Guo
- Department of Pathology, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Chongxiao Qu
- Department of Pathology, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Shilun Feng
- Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Miao Yu
- Department of Research and Development, Stedical Scientific, Carlsbad, California 92010, United States
| | - Hongming Ji
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
| | - Xiang Ren
- Department of Neurosurgery, Shanxi Provincial People's Hospital, The Fifth Clinical Medical College of Shanxi Medical University, Taiyuan, Shanxi 030012, China
- Department of Microelectronics, Tianjin University, Tianjin 300072, China
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Tavakkoli Yaraki M, Tukova A, Wang Y. Emerging SERS biosensors for the analysis of cells and extracellular vesicles. NANOSCALE 2022; 14:15242-15268. [PMID: 36218172 DOI: 10.1039/d2nr03005e] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cells and their derived extracellular vesicles (EVs) or exosomes contain unique molecular signatures that could be used as biomarkers for the detection of severe diseases such as cancer, as well as monitoring the treatment response. Revealing these molecular signatures requires developing non-invasive ultrasensitive tools to enable single molecule/cell-level detection using a small volume of sample with low signal-to-noise ratio background and multiplex capability. Surface-enhanced Raman scattering (SERS) can address the current limitations in studying cells and EVs through two main mechanisms: plasmon-enhanced electric field (the so-called electromagnetic mechanism (EM)), and chemical mechanism (CM). In this review, we first highlight these two SERS mechanisms and then discuss the nanomaterials that have been used to develop SERS biosensors based on each of the aforementioned mechanisms as well as the combination of these two mechanisms in order to take advantage of the synergic effect between electromagnetic enhancement and chemical enhancement. Then, we review the recent advances in designing label-aided and label-free SERS biosensors in both colloidal and planar systems to investigate the surface biomarkers on cancer cells and their derived EVs. Finally, we discuss perspectives of emerging SERS biosensors in future biomedical applications. We believe this review article will thus appeal to researchers in the field of nanobiotechnology including material sciences, biosensors, and biomedical fields.
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Affiliation(s)
- Mohammad Tavakkoli Yaraki
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - Anastasiia Tukova
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
| | - Yuling Wang
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW 2109, Australia.
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Wang BX, Duan G, Xu W, Xu C, Jiang J, Yang Z, Wu Y, Pi F. Flexible surface-enhanced Raman scatting substrates: recent advances in their principles, design strategies, diversified material selections and applications. Crit Rev Food Sci Nutr 2022; 64:472-516. [PMID: 35930338 DOI: 10.1080/10408398.2022.2106547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Surface-enhanced Raman scattering (SERS) is widely used as a powerful analytical technology in cutting-edge areas such as food safety, biology, chemistry, and medical diagnosis, providing ultra-fast, ultra-sensitive, nondestructive characterization and achieving ultra-high detection sensitivity even down to the single-molecule level. Development of Raman spectroscopy is strongly dependent on high-performance SERS substrates, which have long evolved from the early days of rough metal electrodes to periodic nanopatterned arrays building on solid supporting substrates. For rigid SERS substrates, however, their applications are restricted by sophisticated pretreatments for detecting solid samples with non-planar surfaces. It is therefore essential to reassert the principles in constructing flexible SERS substrates. Herein, we comprehensively review the state-of-the-art in understanding, preparing and using flexible SERS. The basic mechanisms behind the flexible SERS are briefly outlined, typical design strategies are highlighted and diversified selection of materials in preparing flexible SERS substrates are reviewed. Then the recent achievements of various interdisciplinary applications based on flexible SERS substrates are summarized. Finally, the challenges and perspectives for future evolution of flexible SERS and their applications are demonstrated. We propose new research directions focused on stimulating the real potential of SERS as an advanced analytical technique for commercialization.
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Affiliation(s)
- Ben-Xin Wang
- School of Science, Jiangnan University, Wuxi, China
| | - Guiyuan Duan
- School of Science, Jiangnan University, Wuxi, China
| | - Wei Xu
- School of Science, Jiangnan University, Wuxi, China
| | - Chongyang Xu
- School of Science, Jiangnan University, Wuxi, China
| | | | | | - Yangkuan Wu
- School of Science, Jiangnan University, Wuxi, China
| | - Fuwei Pi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
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Nam W, Kim W, Zhou W, You EA. A digital SERS sensing platform using 3D nanolaminate plasmonic crystals coupled with Au nanoparticles for accurate quantitative detection of dopamine. NANOSCALE 2021; 13:17340-17349. [PMID: 34585195 DOI: 10.1039/d1nr03691b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
We report a digital surface-enhanced Raman spectroscopy (SERS) sensing platform using the arrays of 3D nanolaminate plasmonic crystals (NLPC) coupled with Au nanoparticles and digital (on/off) SERS signal analysis for the accurate quantitative detection of dopamine (DA) at ultralow concentrations. 3D NLPC SERS substrates were fabricated to support the optically dense arrays of vertically-stacked multi-nanogap hotspots and combined with Raman tag-conjugated Au nanoparticles for NLPC-based dual-recognition structures. We demonstrate that the 3D NLPC-based dual-recognition structures including Au nanoparticle-induced additional hotspots can enable more effective SERS enhancement through the molecular recognition of DA. For the accurate quantification of DA at ultralow concentrations, we conducted digital SERS analysis to reduce stochastic signal variation due to various microscopic effects, including molecular orientation/position variation and the spatial distribution of nanoparticle-coupled hotspots. The digital SERS analysis allowed the SERS mapping results from the DA-specific dual-recognition structures to be converted into binary "On/Off" states; the number of "On" events was directly correlated with low-abundance DA molecules down to 1 pM. Therefore, the digital SERS platform using the 3D NLPC-based dual-recognition structures coupled with Au nanoparticles and digital SERS signal analysis can be used not only for the ultrasensitive, accurate, and quantitative determination of DA, but also for the practical and rapid analysis of various molecules on nanostructured surfaces.
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Affiliation(s)
- Wonil Nam
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Wansun Kim
- Nanobiosensor Team, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea.
| | - Wei Zhou
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Eun-Ah You
- Nanobiosensor Team, Korea Research Institute of Standards and Science, Daejeon 34113, Republic of Korea.
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Wu T, Zheng H, Kou Y, Su X, Kadasala NR, Gao M, Chen L, Han D, Liu Y, Yang J. Self-sustainable and recyclable ternary Au@Cu 2O-Ag nanocomposites: application in ultrasensitive SERS detection and highly efficient photocatalysis of organic dyes under visible light. MICROSYSTEMS & NANOENGINEERING 2021; 7:23. [PMID: 34567737 PMCID: PMC8433429 DOI: 10.1038/s41378-021-00250-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 01/14/2021] [Accepted: 02/02/2021] [Indexed: 05/15/2023]
Abstract
Ternary noble metal-semiconductor nanocomposites (NCs) with core-shell-satellite nanostructures have received widespread attention due to their outstanding performance in detecting pollutants through surface-enhanced Raman scattering (SERS) and photodegradation of organic pollutants. In this work, ternary Au@Cu2O-Ag NCs were designed and prepared by a galvanic replacement method. The effect of different amounts of Ag nanocrystals adsorbed on the surfaces of Au@Cu2O on the SERS activity was investigated based on the SERS detection of 4-mercaptobenzoic acid (4-MBA) reporter molecules. Based on electromagnetic field simulations and photoluminescence (PL) results, a possible SERS enhancement mechanism was proposed and discussed. Moreover, Au@Cu2O-Ag NCs served as SERS substrates, and highly sensitive SERS detection of malachite green (MG) with a detection limit as low as 10-9 M was achieved. In addition, Au@Cu2O-Ag NCs were recycled due to their superior self-cleaning ability and could catalyze the degradation of MG driven by visible light. This work demonstrates a wide range of possibilities for the integration of recyclable SERS detection and photodegradation of organic dyes and promotes the development of green testing techniques.
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Affiliation(s)
- Tong Wu
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Hui Zheng
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Yichuan Kou
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Xinyue Su
- College of Physics, Jilin Normal University, Siping, 136000 China
| | | | - Ming Gao
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Lei Chen
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Donglai Han
- School of Materials Science and Engineering, Changchun University of Science and Technology, Changchun, 130022 China
| | - Yang Liu
- College of Physics, Jilin Normal University, Siping, 136000 China
| | - Jinghai Yang
- College of Physics, Jilin Normal University, Siping, 136000 China
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Nam W, Ren X, Kim I, Strobl J, Agah M, Zhou W. Plasmonically Calibrated Label-Free Surface-Enhanced Raman Spectroscopy for Improved Multivariate Analysis of Living Cells in Cancer Subtyping and Drug Testing. Anal Chem 2021; 93:4601-4610. [DOI: 10.1021/acs.analchem.0c05206] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Wonil Nam
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Xiang Ren
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Inyoung Kim
- Department of Statistics, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jeannine Strobl
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Masoud Agah
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Wei Zhou
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, United States
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Nam W, Zhao Y, Song J, Tali SAS, Kang S, Zhu W, Lezec HJ, Agrawal A, Vikesland PJ, Zhou W. Plasmonic Electronic Raman Scattering as Internal Standard for Spatial and Temporal Calibration in Quantitative Surface-Enhanced Raman Spectroscopy. J Phys Chem Lett 2020; 11:9543-9551. [PMID: 33115232 PMCID: PMC8141369 DOI: 10.1021/acs.jpclett.0c03056] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Ultrasensitive surface-enhanced Raman spectroscopy (SERS) still faces difficulties in quantitative analysis because of its susceptibility to local optical field variations at plasmonic hotspots in metallo-dielectric nanostructures. Current SERS calibration approaches using Raman tags have inherent limitations due to spatial occupation competition with analyte molecules, spectral interference with analyte Raman peaks, and photodegradation. Herein, we report that plasmon-enhanced electronic Raman scattering (ERS) signals from metal can serve as an internal standard for spatial and temporal calibration of molecular Raman scattering (MRS) signals from analyte molecules at the same hotspots, enabling rigorous quantitative SERS analysis. We observe a linear dependence between ERS and MRS signal intensities upon spatial and temporal variations of excitation optical fields, manifesting the |E|4 enhancements for both ERS and MRS processes at the same hotspots in agreement with our theoretical prediction. Furthermore, we find that the ERS calibration's performance limit can result from orientation variations of analyte molecules at hotspots.
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Affiliation(s)
- Wonil Nam
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Yuming Zhao
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Junyeob Song
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Seied Ali Safiabadi Tali
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Seju Kang
- Department of Civil and Environmental Engineering, Institute of Critical Technology and Applied Science Sustainable Nanotechnology Center, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Wenqi Zhu
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Henri J. Lezec
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
| | - Amit Agrawal
- Physical Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
- Institute for Research in Electronics and Applied Physics and Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, USA
| | - Peter J. Vikesland
- Department of Civil and Environmental Engineering, Institute of Critical Technology and Applied Science Sustainable Nanotechnology Center, Virginia Tech, Blacksburg, Virginia, 24061, USA
| | - Wei Zhou
- Department of Electrical and Computer Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA
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